Some questions about traveling with Rail Pass

Hey all. I'm visiting Japan in the winter for a few days and just had a couple questions about traveling. While I'm no newbie to public transportation, I am finding looking up details about japanese public trans very confusing...

Basically, what I have gathered is that buying a JR 7-day pass is ideal. I'll be there for around 7 days, flying in to Tokyo (Havent book flights..so don't know airport yet. But around Tokyo). From there, I want to take a 2-day trip to Kyoto for sure, then return back to Tokyo. That trip alone, from what I gathered, basically is the same price as the 7-day pass. So I am definitely getting it.

My question is, will the JR Pass also cover my other travel? I want to visit the Zao fox village for sure. From what I gather, you must take a bullet train there and then a taxi. Will the JR Pass cover the train ride?

Does it also cover transportation within Tokyo, such as the underground? If not, is there a more cost effective thing to purchase to get around? (Sort of like NYC's unlimited metro card) or is it the same price as taking taxis if you divide it between two people? (Like, in LA, it's often cheaper to take uber than the bus if you have more than 1 person).

I would greatly appreciate the advice! Most things I've found are very outdated, and the language barrier sort of makes it harder. I'm trying to learn as much japanese as possible before the trip, but as of right now my knowledge is very basic (Which also scares me - traveling to more rural parts of Japan. Will I be able to get around?)

I'll probably be asking a few other questions on here..so bare with me!

The JR Pass covers all JR lines nationwide, but only JR. Subways and private trains are not covered. Also, some top of the line services are not covered such as the Nozomi between Tokyo and Hakata, the Mizuho, between Osaka and Kyushu. You can get to a lot of places around Tokyo using JR lines so you can combine your pass with the below Suica card.

If you use http://www.hyperdia.com to look for trains, there's a box that you can check or uncheck for the Nozomi and Mizuho. The Hayabusa which runs from Tokyo to Aomori allows JR Pass use, though. JR East might not have allowed the pass when the Tohoku Shinkansen was new, but they've never updated Hyperdia.

Tokyo transport:
http://www.japan-guide.com/e/e2017.html
I use a Suica card simply because it was available at Narita and included the N'Ex into town at that time. I can recharge it by sticking it and some money into machines at most stations and it's good for 10 years from last use. It doesn't save you any money over paying per ticket, but it's a lot more convenient as you just have to tap it on the turnstiles (wickets) when entering or exiting the station. You can use the Suica or any of the other cards on just about all trains, subways, and buses in multiple cities (including Kyoto and Osaka).
http://www.japan-guide.com/e/e2359_003.html

There is a huge amount of simple and clear advice about the rail passes on the different JR web sites.

The JR pass works on JR trains (and some other bits, but they are not necessary here). So your JR train to get to Zao fox village is a JR train that is covered by the JR pass.

Trains that are not covered include the dozen companies in Tokyo that are not JR (actually more than 12, but you won't find them all). The JR pass will work on the JR trains and that will get you around the whole city. For the last little bit or the most direct route, some of the other rail lines (and other companies - including two different subway companies) provide better options, but you can do pretty well with just the JR pass.

Did you think of looking here: http://www.japan-guide.com/e/e2361.html ?